[2'-Modified oligoribonucleotides, containing 1,2-diol and aldehyde groups. Synthesis and properties].

1,2-Diol-oligoribonucleotides were prepared using fully protected 2'-O-[2-(2,3-dihydroxypropyl)amino-2-oxoethyl]uridine 3'-phosphoramidite. Incorporation of the 2'-modified uridine residue into oligonucleotide chains does not significantly affect the thermal stability of RNA and RNA-DNA duplexes. Periodate oxidation of the 1,2-diol results in reactive 2'-aldehyde oligoribonucleotides. Further application of these oligonucleotides for cross-linking with bacterial ribonuclease P was investigated.

Anticoagulant effects of thioanalogs of thrombin-binding DNA-aptamer and their stability in the plasma.

In order to create effective therapeutically significant oligonucleotide structures, a series of analogs of thrombin-binding aptamer d(GGTTGGTGTGGTTGG) containing thiophosphoryl substitutions were synthesized. The anticoagulation effects of the resultant thrombin-binding aptamer analogs were evaluated and the effects of local thiomodifications on their structure and function were studied, including the effects on stability in blood plasma and resistance to DNA nucleases. A promising modified oligonucleotide (LL11) was found with the structure modified only in TT loops. It retains antithrombin properties of thrombin-binding aptamer, but is more resistant to biodegradation.

Byproduct with altered fluorescent properties is formed during standard deprotection step of hexachlorofluorescein labeled oligonucleotides.

HEX-labeled oligonucleotides obtained via typical synthetic protocols may contain more than 15% of material with altered spectral characteristics. We discovered hexachlorofluorescein residue transformation unknown earlier for standard DNA ammonolysis step. HEX residue reacts with ammonium hydroxide yielding acridine derivative, which has differed UV-VIS and fluorescent properties compared to HEX. Therefore, for critical bioassays where sensitivity and/or fluorescent signal differentiation (e.g., in quantitative or multiplexed assays) are essential, the careful RP-HPLC purification step is required.

[Oligodeoxynucleotides containing substituted 4-nitroindoles: synthesis and study of their DNA duplexes].

The synthesis of oligonucleotides containing 1-(2-deoxy-beta-D-ribofuranosyl)-2-methyl-4-nitroindole and 1-(2-deoxy-beta-D-ribofuranosyl)-2-phenyl-4-nitroindole is described. The synthesized modified oligonucleotides were used for studying the stability of intermolecular DNA duplexes with one unnatural strand and for evaluation of discriminating potential of 2-methyl- and 2-phenyl-4-nitroindoles toward nucleic bases. For comparison, an unmodified oligonucleotide and oligonucleotides bearing 5-nitroindole were used. It was shown that 2-methyl-4-nitroindole was only insignificantly inferior in stability to 5-nitroindole and characterized by a similar discriminating potential. 2-Phenyl-4-nitroindole provided a more pronounced duplex destabilization, the discrimination toward natural bases being decreased. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2008, vol. 34, no. 2; see also http:// www.maik.ru.

[Conformational polymorphysm of G-rich fragments of DNA Alu-repeats. II. the putative role of G-quadruplex structures in genomic rearrangements]. / Konformatsionnyi polimorfizm G-bogatykh fragmentov ALU-povtorov DNK. II. potentsial'naia rol' G-kvadrupleksnykh struktur v genomnykh perestroikakh.

Three evolutionary conserved sites of Alu repeats (PQS2, PQS3 and PQS4) were shown to form stable inter- and intramolecular G-quadruplexes (GQs) in vitro. Structures and topologies of these GQs were elucidated using spectral methods. Self-association of G-rich Alu fragments was studied. Dimeric GQ formation from two distal identical or different putative quadruplex sites - (PQS2)2, (PQS3)2 or PQS2-PQS3 - within one lengthy DNA strand was demonstrated by a FRET-based method. Oligomer PQS4 (folded into a parallel intramolecular GQ) was shown to form stacks of quadruplexes that are stabilized by stacking interactions of external G-tetrads (this was confirmed by DOSY NMR, AFM microscopy and differential CD spectroscopy). Comparative analysis of the properties of various GQs allowed us to put forward a hypothesis of two general mechanisms of intermolecular GQ-dependant genomic rearrangements: 1) formation of a dimeric GQs; 2) association of pre-folded intramolecular parallel GQs from different strands into GQ-stacks. Thus, the observed co-localization of G-rich motifs of Alu elements with double-strand break hotspots and rearrangement hotspots may be accounted for by the specific secondary structure of these motifs. At the same time, this is likely primarily due to high abundance of such G-rich Alu fragments in the genome.

[Conformational polymorphysm of G-rich fragments of DNA ALU-repeats. I. Potential noncanonical structures]. / Konformatsionnyi polimorfizm G-bogatykh fragmentov ALU-povtorov DNK. I. Nekanonicheskie struktury.

In this paper, we report results of systematic studies of conformational polymorphism of G-rich DNA fragments from Alu repeats. Alu retrotransposones are primate-specific short interspersed elements. Using the Alu sequence from the prooncogen bcl2 intron and the consensus AluSx sequence as representative examples, we determined characteristic Alu sites that are capable of adopting G-quadruplex (GQ) conformations (i.e., potential quadruplex sites - PQSAlu), and demonstrated by bioinformatics methods that those sites are Alu-specific in the human genome. Genomic frequencies of PQSAlu were assessed (~1/10000 b.p.). The sites were found to be characteristic of young (active) Alu families (Alu-Y). A recombinant DNA sequence bearing the Alu element from the human bcl2 gene (304 b.p.) and its PQS-mutant (Alu-PQS) were constructed. The formation of noncanonical structures in Alubcl2 dsDNA and the absence of such structures in the case of Alu-PQS were shown using DMS-footprinting and AFM microscopy. Expression vectors bearing wild-type and mutant Alu insertions in the promoter regions were obtained, and the effects of these insertions on the expression of the reporter gene in НЕК293 and HeLa cell lines were compared. Our findings on the spatial organization of Alu repeats may provide insight into the mechanisms of genomic rearrangements which underlie many oncological and neurodegenerative diseases.

Chaos-induced intensification of wave scattering.

Sound-wave propagation in a strongly idealized model of the deep-water acoustic waveguide with a periodic range dependence is considered. It is investigated how the phenomenon of ray and wave chaos affects the sound scattering at a strong mesoscale inhomogeneity of the refractive index caused by the synoptic eddy. Methods derived in the theory of dynamical and quantum chaos are applied. When studying the properties of wave chaos we decompose the wave field into a sum of Floquet modes analogous to quantum states with fixed quasi-energies. It is demonstrated numerically that the "stable islands" from the phase portrait of the ray system reveal themselves in the coarse-grained Wigner functions of individual Floquet modes. A perturbation theory has been derived which gives an insight into the role of the mode-medium resonance in the formation of Floquet modes. It is shown that the presence of a weak internal-wave-induced perturbation giving rise to ray and wave chaos strongly increases the sensitivity of the monochromatic wave field to an appearance of the eddy. To investigate the sensitivity of the transient wave field we have considered variations of the ray travel times--arrival times of sound pulses coming to the receiver through individual ray paths--caused by the eddy. It turns out that even under conditions of ray chaos these variations are relatively predictable. This result suggests that the influence of chaotic-ray motion may be partially suppressed by using pulse signals. However, the relative predictability of travel time variations caused by a large-scale inhomogeneity is not a general property of the ray chaos. This statement is illustrated numerically by considering an inhomogeneity in the form of a perfectly reflecting bar.

Theory and applications of ray chaos to underwater acoustics.

Chaotic ray dynamics in deep sea propagation models is considered using the approaches developed in the theory of dynamical chaos. It has been demonstrated that the mechanism of emergence of ray chaos due to overlapping of nonlinear ray-medium resonances should play an important role in long range sound propagation. Analytical estimations, supported by numerical simulations, show that for realistic values of spatial periods and sound speed fluctuation amplitudes associated with internal-wave-induced perturbations, the resonance overlapping causes stochastic instability of ray paths. The influence of the form of the smooth unperturbed sound speed profile on ray sensitivity to the perturbation is studied. Stability analysis has been conducted by constructing the Poincaré maps and examining depth differences of ray trajectories with close take-off angles. The properties of ray travel times, including fractal properties of the time front fine structures, under condition of ray chaos have been investigated. It has been shown that the coexistence of chaotic and regular rays, typical for dynamical chaos, leads to the appearance of gaps in ray travel time distributions, which are absent in unperturbed waveguides. This phenomenon has a prototype in theory of dynamical chaos called the stochastic particle acceleration. It has been shown that mesoscale inhomogeneities with greater spatial scales than that of internal waves, create irregular local waveguide channels in the vicinity of the axis (i.e., sound speed minimum) of the unperturbed waveguide. Near-axial rays propagating at small grazing angles, "jump" irregularly between these microchannels. This mechanism determines chaotic behavior of the near-axial rays.

Sensitivity of ray travel times.

Ray in a waveguide can be considered as a trajectory of the corresponding Hamiltonian system, which appears to be chaotic in a nonuniform environment. From the experimental and practical viewpoints, the ray travel time is an important characteristic that, in some way, involves an information about the waveguide condition. It is shown that the ray travel time as a function of the initial momentum and propagation range in the unperturbed waveguide displays a scaling law. Some properties of the ray travel time predicted by this law still persist in periodically nonuniform waveguides with chaotic ray trajectories. As examples we consider few models with special attention to the underwater acoustic waveguide. It is demonstrated for a deep ocean propagation model that even under conditions of ray chaos the ray travel time is determined, to a considerable extent, by the coordinates of the ray endpoints and the number of turning points, i.e., by a topology of the ray path. We show how the closeness of travel times for rays with equal numbers of turning points reveals itself in ray travel time dependencies on the starting momentum and on the depth of the observation point. It has been shown that the same effect is associated with the appearance of the gap between travel times of chaotic and regular rays. The manifestation of the stickiness (the presence of such parts in a chaotic trajectory where the latter exhibits an almost regular behavior) in ray travel times is discussed. (c) 2002 American Institute of Physics.

[Compounds similar to acyclovir. I. Synthesis of "complete" analogs of nucleosides]. / Soedineniia, podobnye atikloviru. I. Sintez "polnykh" atiklicheskikh analogov nukleozidov.

"Full" acyclic analogues of ribonucleosides, 1-(1,2,6-trihydroxy-4-oxahex-3-yl)thymine and -cytosine, 3- and 9-(1,2,6-trihydroxy-4-oxahex-3-yl)adenine, and 9-(1,2,6-trihydroxy-4-oxahex-3-yl)guanine, have been prepared by condensation of silylated nucleo-bases with 1,4,5,6-tetraacetoxy-3-oxahexane in the presence of Lewis acids followed by deacetylation.

[Compounds similar to acyclovir. II. Synthesis of acyclic analogs of 2'-deoxynucleosides]. / Soedineniia, podobnye atsikloviru. II. Sintez atsiklicheskikh analogov 2'-deoksinukleozidov.

Acyclic analogues of nucleosides, viz.9- and 3-(1,6-dihydroxy-4-oxahex-3-yl)adenine, 9-(1,6-dihydroxy-4-oxahex-3-yl)guanine, 1-(1,6-dihydroxy-4-oxahex-3-yl)cytosine and thymine, with C3'-C4' bond of the furanose ring cleaved, have been prepared by condensation of trimethylsilyl derivatives of nucleic acid bases with 1,4,6-triacetoxy-3-oxahexane in the presence of Lewis acids followed by treatment with metanolic ammonia.

[Compounds similar to acyclovir. III. Synthesis of acyclic analogs of 5'-deoxynucleosides]. / Soedineniia, podobnye atikloviru. III. Sintez atsiklicheskikh analogov 5'-dezoksinukleozidov.

A convenient method has been proposed for the synthesis of 1,2-dihydroxy-4-oxahex-3-yl and 1-hydroxy-4-oxahex-3-yl derivatives of guanine, adenine, thymine and cytosine, acyclic nucleoside analogues lacking the 3'--4' bond.

[Acyclic analogs of ribavirin. Synthesis and antiviral activity]. / Atsiklicheskie analogi ribavirina. Sintez i protivovirusnaia aktivnost'.

Activity of several ribavirin analogues, viz.1-(2-hydroxyethoxymethyl)-, 1-(3-hydroxypropoxymethyl)-, 1-(4-hydroxybutoxymethyl)- and 1-(2,3-dihydroxypropyl)-1,2,4-triazole 5- and 3-carboxamides, against human adenovirus type 2 in the Hep-2 cell culture has been studied. The ether oxygen atom imitating the ribose O4' was shown to be essential for the antiviral activity. 1-(2-Hydroxyethoxymethyl)-1,2,4-triazole 3-carboxamide, a structural analogue of ribavirin in which the hydroxyl group is apparently equivalent to the ribose 5'-OH, possesses the highest activity among the compounds studied. Lengthening of the alkyl side chain reduces essentially the antiviral activity.

[A simple, convenient method for the synthesis of acyclic analogs of guanosine]. / Prostoi, udobnoyi metod sinteza atsiklicheskikh analogov guanozina.

A simple convenient method for the synthesis of guanosine acyclic analogues with the nucleic base attached to the primary carbon atom is proposed. The method involves treatment of trimethylsilyl derivative of guanine with agents of general formula ROCH2Cl in the absence of Lewis acids. 9-Substituted derivatives of guanine were prepared by this method with 50-65% yields.

[Synthesis and properties of acyclic analogs of ribavirin]. / Sintez i svoistva atsiklicheskikh analogov ribavirina.

Acyclic analogues of ribavirine, viz. 1-(1-hydroxy-4-oxahex-3-yl)-, 1-(1-chloro-4-oxahex-3-yl)-, 1-(1,2-dihydroxy-4-oxahex-3-yl)-, 1-(1,6-dihydroxy-4-oxahex-3-yl)-, 1-(1-chloro-6-hydroxy-4-oxahex-3-yl)-, and 1-(1,2,6-trihydroxy-4-oxahex-3-yl)-1,2,4-triazole-3-carboxamide, with the C3'-C4' bond of the furanose ring cleaved, have been prepared by condensation of trimethylsilyl derivatives of 3-ethoxycarbonyl-1,2,4-triazole with alkylating agents in the presence of SnCl4 followed by treatment with methanolic ammonia. Convenient methods for synthesis of the alkylating agents were elaborated.

[Compounds similar to acyclovir. IV. A convenient method of synthesizing adenallene]. / Soedineniia, podobnye atsikloviru. IV. Udobnyi metod sinteza adenallena.

A convenient method for the synthesis of adenallen (9-(4-hydroxy-1,2-butadienil)adenine) is proposed. Adenallen was prepared in 30% yield by alkaline treatment of 9-(4-acetoxy-2-butinyl)adenine synthesized, in turn, by condensation of sodium derivative of adenine with 4-acetoxy-1-chlorbutine-2.

[Compounds, similar to acyclovir. VIII. Synthesis and antiviral activity of (R/S)-5-hydroxy-4-hydroxymethyl-3-oxapent-2-yl derivatives of nucleic bases]. / Soedineniia, podobnye atsikloviru. VIII. Sintez i protivovirusnaia aktivnost' (R/S)-5-gidroksi-4-gidroksimetil-3-oksapent-2-il'nykh proizvodnykh nucleinovykh osnovanii.

The (R/S)-5-hydroxy-4-hydroxymethyl-3-oxapent-2-yl derivatives of the uracil, thymidine, cytosine, adenine, guanine and 1,2,4-triazol-3-carboxamide were synthesized using 1,3-diacetoxy-2-(1-acetoxy)propane and 1,3-dichloro-2-(1-chlorethoxy)propane as alkylating agents. The guanine derivatives exhibited activity against HSV-1 (chemotherapeutic index 32).

[Compounds similar to acyclovir. VI. Synthesis of optically active 1',2'-seconucleosides]. / Soedineniia, podobnye atsikloviru. VI. Sintez opticheski aktivnykh 1',2'-sekonukleozidov.

A convenient method is suggested of synthesis of (3R, 4R)-, (3S, 4S)- and (3R/S, 4S/R)-dihydroxy-3-hydroxymethyl-2-oxapentyl derivatives of the, cytosine, uracyl, adenine and guanine ("full" acyclic analogues of nucleosides with C1'-C2' bond cleaved) by condensation of trimethylsilyl derivatives of nucleic bases (sodium salt in case of adenine) with (3$, 4R)-, (3S )-, (3S, 4S)- and (3R/S, 4S/R)-4,5-diacetoxy-3-acetoxymethyl-1-chloro-2-oxapentanes without catalyst followed by deacetylation.

[Compounds similar to acyclovir. VII. Attempts to construct an anti-herpetic agent (6-hydroxy-2-oxa-4-hexenyl derivatives of nucleic bases]. / Soedineniia, podobnye atsikloviru. VII. Popytka konstruirovaniia protivogerpeticheskogo preparata (6-gidroksi-2-oksa-4-geksenil'nye proizvodnye nukleinovykh osnovanii.

Based on the available data on the acyclovir's mechanism of action we attempted to predict the antiherpetic activity of 6-hydroxy-2-oxahexen-4-yl derivatives of nucleic bases. In terms of this model 9-(6-hydroxy-2-oxahexen-4-yl) guanine might be active. 6-Hydroxy-2-oxahexen-4-yl derivatives of adenine, guanine, cytosine, thymine, uracil, 1,2,4-triazole-3 and 1,2,4-triazole-5-carboxamide have been synthesized and their activity against herpes virus I investigated. The guanine derivative proved to possess rather high activity (chemotherapeutical index 8).

[Compounds, similar to acyclovir V. Synthesis and antiviral activity of carbethoxyalkoxymethyl derivatives of nucleic bases]. / Soedineniia, podobnye atsikloviru V. Sintez i protivovirusnaia aktivnost' karbétoksialkoksimetil'nykh proizvodnykh nukleinovykh osnovanii.

Ethyl esters and amides of carboxymethoxy-, alpha- and beta-carboxyethoxy- and gamma-carboxypropoxymethyl derivatives of adenine, guanine, cytosine, uracil, thymine, 1,2,4-triazole-3- and -5-carboxamide were synthesized and their antiviral activity was studied.